In vitro method for identifying compounds for cancer therapy

ABSTRACT

The present invention relates to an in vitro method for identifying and evaluating compounds useful in the treatment of different types of cancer, especially lung, breast, colorectal and bladder cancer in an individual, for determining the stage or severity of said cancer in the individual, or for monitoring the effect of the therapy administered to an individual having said cancer; to finding, identifying, developing and evaluating the efficacy of compounds for the therapy of said cancer, for the purpose of developing new medicinal products; as well as to agents inhibiting the expression and/or activity of the choline kinase alpha protein and/or the effects of this expression.

FIELD OF THE INVENTION

The present invention relates to a method for identifying and evaluatingthe efficacy of compounds for cancer therapy, especially for lung,breast or colorectal cancer, for the purpose of developing new medicinalproducts; as well as to agents inhibiting the expression and/or theactivity of the choline kinase alpha protein and/or the effects of thisexpression.

BACKGROUND OF THE INVENTION

Choline kinase (also known as CK, CHK and ChoK) is the initial enzyme ofthe Kennedy or phosphatidylcholine (PC) synthesis pathway andphosphorylates choline to phosphorylcholine (PCho) in the presence ofmagnesium (Mg²⁺) using adenosine 5′-triphosphate (ATP) as a phosphategroup donor. The transformation mediated by various oncogenes induceshigh levels of choline kinase activity, giving rise to an abnormalincrease in the intracellular levels of its product, PCho, whichindirectly supports the role of choline kinase in generating humantumors. However, there are alternative PCho generation mechanisms thatdo not involve the activation of choline kinase and could explain thehigh levels of this metabolite in tumor cells.

Although there is evidence of increase in activity of the enzyme cholinekinase in tumors and transformed cells, its relationship to thecarcinogenic process is not sufficiently demonstrated as no clearcause-effect relationship has been established between the increase inactivity and the tumor transformation. On the other hand, the moleculeresponsible for this effect has still not been identified.

About 200 gene sequences encoding for polypeptides with a primarystructure homologous to choline kinase have been identified and aredesignated as choline kinase alpha a, choline kinase alpha b, cholinekinase alpha 3, choline kinase beta 1, choline kinase beta 2, cholinekinase CKB-1 Choline/ethanolamine kinase, choline kinase-likeethanolamine kinase, Cots, Duff227, Cog3173 CPTlB, SFl, SHOX2, FHOD2,FLJ12242, KRT5, FBL, ARL6IP4, etc. (seehttp://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi#219541) both in humans andin other mammals and rodents (rats, mice, cows, guinea pigs, rabbits,monkeys). In fact, since 1982 there has been biochemical evidence thatin different tissues isolated from rats, mice and humans there are atleast three isoenzymes with choline kinase activity showing differentphysicochemical properties.

At least 3 genes encoding for proteins with demonstrated choline kinaseactivity have recently been identified in human genoma, designated asck-alpha, ck-beta, and HCEKV (USA patent US2003186241), and severalgenes the encoded proteins of which are 30-65% homologous to thoseencoded by the ck genes, such as for example the genes CAI16602, CHKL,CAI16600, CAI16599, CAH56371, CAIl6603, BAA91793, CAI16598 described in(http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi), and the genes CPTlB,EKI2, SFl, SHOX2, FHOD2, FLJ12242, KRT5, FBL, ARI6lp$, TOMM40, MLL,described in(http://www.ebi.ac.uk/cgi-bin/sumtab?tool=asdblast&jobid=blast-20050412-18072127).A very relevant characteristic of the different choline kinaseisoenzymes is that they have different biochemical properties, withimportant variations in their affinity for the choline substrate or forthe ATP phosphate donor, and even in their active form, which can bepresented as dimers or tetramers. Therefore it is necessary to define ifthere is a direct relationship between any of the different cholinekinase isoenzymes identified and the attributed tumorigenic capacity dueto their overexpression in human tumors.

On the other hand, choline kinase inhibition has been demonstrated to bea new and effective anti-tumor strategy in cells transformed byoncogenes, which has been extrapolated to nude mice in vivo. Theincrease in choline kinase activity in several human breast carcinomashas recently been published, and it has been seen that the cholinekinase alteration is a frequent event in some human tumors such as lung,colorectal and prostate tumors.

Despite the correlation between some parameters and others, there iscurrently no evidence definitely establishing that the overexpression ofcholine kinase has oncogenic and tumor activity in human cells. There isevidence indicating that choline kinase activity inhibitors, such ashemicholinium-3 [Cuadrado A., Carnero A., Dolfi F., Jiménez B. and LacalJ. C. Oncogene 8, 2959-2968 (1993); Jiménez B., del Peso L., MontanerS., Esteve P. and Lacal J. C. J. Cell Biochem. 57, 141-149 (1995);Hernández-Alcoceba, R., Saniger, L., Campos, J., Núñez, M. C., Khaless,F., Gallo, M. Á., Espinosa, A, Lacal, J. C. Oncogene, 15, 2269-2301(1997)] or the low-toxicity methylenequinones in Spanish patentapplication ES200503263, present anti-tumor activity. However, there isno conclusive evidence in the mentioned documents or in the rest of theprior art as regards to the various isoenzymes with demonstrated cholinekinase activity (ck-alpha, ck-beta, HCEKV, etc) and identified in humantissues could be responsible for the detected enzymatic activity, nor isit indicated which of the isoenzymes is sensitive to the inhibition byinhibitors which have shown anti-tumor activity. This identification isnecessary in order to be able to establish its potential use as atherapeutic target in cancer.

OBJECT OF THE INVENTION

The main object of the present invention is an in vitro method to find,identify and evaluate the effectiveness of compounds for cancer therapy,especially for lung, breast or colorectal cancer.

A further object of the invention is based on the use of nucleotide orpeptide sequences derived from the choline kinase alpha gene in methodsfor finding, identifying, developing and evaluating the effectiveness ofcompounds for cancer therapy, preferably for lung, breast or colorectalcancer.

Another object of the present invention consists of providing agentscharacterized in that they inhibit the expression and/or the activity ofthe choline kinase alpha protein for the treatment of cancer, preferablylung, breast or colorectal cancer.

Another object of the invention is a pharmaceutical compositioncomprising one or several therapeutic agents together with apharmaceutically acceptable excipient for the treatment of cancer,preferably lung, breast or colorectal cancer.

An in vitro method for monitoring the effect of a therapy administeredto a cancer patient is also object of the present invention,characterized in that the evaluation of the choline kinase alpha proteinexpression level in a tissue sample extracted from the patient who isbeing administered an anti-tumor agent, preferably an agent according toclaims 3-5, by means of the determination in said sample of at least oneparameter related to the choline kinase alpha protein which is selectedfrom the level of its messenger RNA, the concentration of said proteinor its enzymatic activity, and the comparison of the value obtained withthe value corresponding to one or more normal, non-cancerous tissuesamples.

Finally, another object of the present invention consists of adiagnostic kit to carry out the present invention.

DESCRIPTION OF FIGURES

FIG. 1: A) Choline kinase activity (ChoK) in human Hek2931 cell (Humanembryonic kidney cells) extracts after overexpressing choline kinasealpha and beta (ex vivo choline kinase activity assay). B) Intracellularphosphorylcholine levels in live cells (in vitro choline kinase activityassay).

FIG. 2: A) ChoK activity in human Chok293T cells after overexpressingcholine kinase alpha and beta. B) Specificity of the monoclonalantibodies generated against choline kinase alpha in the same extractsshown in A.

FIG. 3: Choline kinase alpha overexpression determined by means ofimmunohistochemical techniques in NSCLC (Non-small cell lung cancer).

FIG. 4: Choline kinase alpha overexpression determined by means ofimmunohistochemical techniques in breast cancer.

FIG. 5: Choline kinase alpha overexpression determined by means ofimmunohistochemical techniques in colon cancer. B) Polyp in which theprogressive staining is observed from the pre-neoplastic lesions to themass of the tumor.

FIG. 6: Attachment-independent growth of cells overexpressing humancholine kinase alpha. Both the number of colonies generated and therelative size thereof in the two cell lines analyzed, Hek293 and MDCK,are shown.

FIG. 7: In vivo oncogenic activity of choline kinase alpha in Nu/Numice.

FIG. 8: Expression and enzymatic activity of choline kinase alpha intumors induced in vivo.

FIG. 9: Specificity of the inhibitor MN58b on choline kinase alpha. E.coil extracts in which recombinant human choline kinase alpha or cholinekinase beta proteins are expressed were analyzed in the absence (0) orin the presence of increasing concentrations of MN58b.

FIG. 10: Anti-tumor effect of the inhibitor MN58b on tumors induced bycholine kinase alpha overexpression

FIG. 11: Blocking of choline kinase alpha expression by the siRNAtechnique in human HeK293T cells.

FIG. 12: Blocking of choline kinase alpha expression by means of siRNAin tumor cells derived from a human breast carcinoma, determined both byWestern Blotting A) and B) and by enzymatic activity C).

FIG. 13: Death due to apoptosis induced by specific interference RNA ofcholine kinase alpha in human breast tumor cells MDA-MB-231. A) Flowcytometry analysis with propidium iodide. B) Digestion of WARPassociated to death due to apoptosis.

FIG. 14: specific interference RNA of choline kinase alpha in primaryhuman mammary epithelial cells HMEC. A) Basal choline kinase alphaexpression levels in normal HMEC cells with respect to the tumor cellsMDA-MB-231. B) Interference with choline kinase alpha in HMEC. C) Theinterference of choline kinase alpha does not induce cell death inprimary human HMEC cells.

FIG. 15: Choline kinase alpha overexpression in breast cancer tissue.FIG. 15 a: choline kinase alpha messenger RNA in tissues of patientswith breast cancer detected by real-time quantitative PCR, representedas the base 10 logarithm between the amount detected and the amountpresent in a normal tissue sample. FIG. 15 b: mean value of cholinekinase alpha expression, represented as the relative expression units ofthe gene calculated from the mRNA level with the 2^(−ΔΔct) method) inindividuals without metastasis (first bar, marked as “NO”) or withmetastasis (second bar, marked as “YES”). FIG. 15 c: evolution of theprobability of survival without disease according to the number ofelapsed months in the patients with lymphatic nodes (lower line, markedwith gray strokes, †) or without lymphatic nodes (upper line, markedwith black strokes, †).

FIG. 16: Choline kinase alpha expression in cell lines derived from lungcancer. FIG. 16 a: choline kinase alpha messenger RNA in cell linesderived from NSCLC (H1299 and H460) or SCLC (H510 and H82) type cancer,detected by real-time quantitative PCR, represented as the base 10logarithm of the ratio between the amount detected and the amountpresent in normal primary bronchial epithelial cells (EEC). FIG. 16 b:choline kinase alpha protein detected by immunoassay with a monoclonalantibody in normal bronchial epithelial cells (BEC) and in cell linesderived from lung cancer H460, H1299, H510 and H82; the signal obtainedfor tubulin in these same samples is represented immediately under that.FIG. 16 c: choline kinase activity represented by the radioactivelymarked PCho signal, detected per microgram of protein after 30 minutes,generated from choline marked in each of the cell lines indicated underthe corresponding bars.

FIG. 17: Choline kinase alpha messenger RNA expression in tissue oftumors extracted from patients with lung cancer NSCLC in early stages,detected by real-time quantitative PCR, represented as base 10 logarithmof the ratio between the amount detected and the amount present in anormal tissue sample.

FIG. 18: Evolution of the probability of survival of patients with lungcancer over time, represented in months, in the event that cholinekinase alpha expression is detected (dashed lines, -†-) or not detected(continuous lines, †). The overall survival of patients in stages I toIV (graph located in the upper left part), disease-free survival ofpatients in stages I to IV (time elapsing from when the patients areoperated on until they have a relapse) (graph located in the lower leftpart), survival in the case of cancer in stages IA-IIIA (graph locatedin the upper right part) and disease-free survival in the case of stagesIA-IIIA (graph located in the lower right part).

FIG. 19: Choline kinase alpha expression in cell lines derived frombladder cancer. FIG. 19 a: Choline kinase alpha messenger RNA in celllines derived from bladder cancer detected by real-time quantitativePCR, represented as base 10 logarithm 10 of the ratio between the amountdetected and the amount present in normal immortalized bladder UrotSacells; from left to right, the bars correspond to lines ET1376, J82,SW780, TCCSup and UMVC3. FIG. 19 b: choline kinase alpha proteindetected by immunoassay with a monoclonal antibody in normalimmortalized bladder cells (UrotSa) and in cell lines derived frombladder cancer TCCsup, J82, UMVC3, SW789 and HT1376, as well as in anegative control (Hek293T cells) and in a positive control (Hek-ChoKcells, transfected with a plasmid expressing choline kinase alpha); thesignal obtained for tubulin in the same samples is representedimmediately under it. FIG. 16 c: choline kinase activity represented bythe radioactively marked PCho signal detected per microgram of proteinafter 30 minutes, generated from choline, marked in each of the celllines indicated under the corresponding bars.

FIG. 20: Choline kinase alpha expression in patients with bladdercancer. FIG. 20 a: Mean expression values obtained from tumor tissues in90 patients by means of microarray U133 Plus 2.0 of Affymetrix, obtainedin the different groups classified according to the value of theinduction factor: an induction of 1 to 3 times (first bar), an inductionof 3 to 8 times or an induction of 8 to 24 times (third bar). FIG. 20 b:choline kinase alpha messenger RNA in 20 patients with bladder cancer,detected by real-time quantitative PCR, represented as base 10 logarithmof the ratio between the amount detected and the amount present inimmortalized normal bladder UrotSa cells; the horizontal line representsthe level from which there is an association with a worse prognosticevolution of the patient.

FIG. 21: Relationship between choline kinase alpha expression and thepresence of nodes and/or metastasis. FIG. 21 a: Mean choline kinasealpha expression levels in negative and positive patients with respectto the presence of lymphatic nodes (values marked with empty boxes,) ormetastasis (values marked with solid circles, ); the straight linesjoin the mean values corresponding to positive or negative individualswith respect to the characteristic considered to aid in seeing thedifference in level between the groups), FIG. 21 b: proportion ofpatients with metastases (bars with continuous dark color,

) and without metastases (bars with slash marks, //) in groups ofpatients classified according to the choline kinase alpha expressionlevel: low (pair of bars on the left), intermediate (pair of barslocated in the middle of the graph) or high (pair of bars located on theright side of the graph).

FIG. 22: Operating scheme of the construction based on whichinterference RNA can be synthesized. In the presence of repressor (leftarea, “No Expression”, it binds to the construction and prevents RNAsynthesis); in the presence of an inducer (doxocycline), it binds to therepressor, preventing its attachment to the interference constructionand allowing synthesis of the interference RNA (right area,“Expression”).

FIG. 23: Proliferation of MDA-MB-231 (upper row of plaques) and Ch-ind-1(lower row of plaques) cells in growth permissive conditions (“Control”column? or in the presence of the chemical inhibitors of choline kinaseMN58b (middle column) or RSM936 (right column).

FIG. 24: Behavior or MDA-MB—231 (bars marked as “MDA”) and Ch-ind-1(bars marked as “Chindl”) cells in the absence (“-”) or presence “+” of10 μg/ml of doxocycline, after 10 days (“10 d”) or 20 days (“20 d”). A:Effect on the genetic inhibition of choline kinase alpha according tothe ratio between the choline kinase alpha and GAPDH levels; B: Effecton cell proliferation, according to the ratio between the pCNA and GAPDHlevels; C: Cell viability of the Ch-ind-1 cells in the absence (dottedline) or in the presence (continuous line) of an inducer, deduced fromthe absorbance values at 500 nm observed at different times; D: Effecton apoptosis induction, according to the ratio between the degraded PARPprotein level with respect to the total PARP protein level(PARPdig/PARPtotal).

FIG. 25: Specificity of the polyclonal antibody against choline kinasebeta. A: Immunoassay in which an anti-choline kinase beta polyclonalantiserum interacts with samples of cells transfected with an emptyvector (lane called “empty”), a choline kinase alpha expression vector(lane called “ChoKA”), a choline kinase beta expression vector (lanecalled “ChoKB”) and a chimeric protein, choline kinase beta-greenfluorescent protein, expression vector (lane called “ChoK35′ GFP”). Thearrows indicate the banding height of choline kinase beta and of thechimeric protein. B: Immunoassay in which an anti-choline kinase alphapolyclonal antibody interacts with samples of cells transfected with anempty vector (lane called “empty”), a choline kinase alpha expressionvector (lane called “ChoKA”), a choline kinase beta expression vector(lane called “ChoKB”) and a chimeric protein, choline kinasebeta—fluorescent green protein, expression vector (lane called“ChoKB5′GFP”). The arrows indicate the banding height of choline kinasealpha.

FIG. 26: Comparison of the tumorigenic capacity of choline kinases alphaand beta. Evolution of the tumor volume, measured in square centimeters;according to the weeks indicated on the x-axis, elapsing from theinjection in mice of cells transfected with: an empty vector (dataindicated with diamonds “♦”), a choline kinase alpha expression vector(data indicated with squares, “▪”), a choline kinase beta expressionvector (data indicated with triangles, “ ”) and a choline kinase alphaexpression vector+a choline kinase beta expression vector (dataindicated with an x, “X”).

FIG. 27: Choline kinase beta messenger RNA in tissue of patients withlung cancer, detected by real-time quantitative PCR, represented as base10 logarithm of the ratio between the amount detected and the amountpresent in normal tissue.

DETAILED DESCRIPTION OF THE INVENTION

To facilitate understanding the present patent application, the meaningof some terms and expressions shall be defined below within the contextof the invention:

The terms “subject” or “individual” refer to members of mammal animalspecies and includes but is not limited to domestic animals, primatesand humans; the subject is preferably a male or female human being ofany age or race.

The term “cancer” refers to the disease that is characterized by anabnormal or uncontrolled growth of cells capable of invading adjacenttissues and spreading to distant organs.

The term “carcinoma” refers to the tissue resulting from the abnormal oruncontrolled cell growth.

The term “breast cancer” or “breast carcinoma” refers to any malignantproliferative mammary cell disorder.

The term “colon cancer” or “colon carcinoma” refers to any malignantproliferative colon cell disorder.

The term “rectal cancer” or “rectal carcinoma” refers to any malignantproliferative rectal cell disorder.

The term “tumor” refers to any abnormal tissue mass resulting from abenign (non-cancerous) or malignant (cancerous) neoplastic process.

The term “gene” refers to a deoxyribonucleotide molecular chain encodinga protein.

The term “DNA” refers to deoxyribonucleic acid. A DNA sequence is adeoxyribonucleotide sequence.

The term “cDNA” refers to a complementary nucleotide sequence of an mRNAsequence.

The term “RNA” refers to ribonucleic acid. An RNA sequence is aribonucleotide sequence.

The term “mRNA” refers to messenger ribonucleic acid, which is thefraction of total RNA which translates proteins.

The term “mRNA transcribed from” refers to the transcription of the gene(DNA) in mRNA as a first step so that the gene is expressed andtranslated to a protein.

The term “nucleotide sequence” or “nucleotidic sequence” indistinctlyrefers to a ribonucleotide (RNA) or a deoxyribonucleotide (DNA)sequence.

The term “protein” refers to a molecular amino acid chain, attached bycovalent or non-covalent bonds. The term includes all forms ofpost-translational modifications, for example glycosylation,phosphorylation or acetylation.

The terms “peptide” and “polypeptide” refer to molecular amino acidchains representing a protein fragment. The terms “protein” and“peptide” are used indistinctly.

The term “antibody” refers to a glycoprotein exhibiting specific bindingactivity for a target molecule, which is referred to as “antigen”. Theterm “antibody” comprises monoclonal antibodies or polyclonalantibodies, either intact or fragments thereof; and it includes humanantibodies, humanized antibodies and antibodies of non-human origin.“Monoclonal antibodies’” are homogenous populations of highly specificantibodies which are directed against a single antigen site or“determinant”. “Polyclonal antibodies” include heterogeneous populationsof antibodies which are directed against different antigen determinants.

The term “epitope”, as it is used in the present invention, refers to anantigen determinant of a protein, which is the amino acid sequence ofthe protein that a specific antibody recognizes.

The term “therapeutic target” refers to nucleotide or peptide sequencesagainst which a drug or therapeutic compound can be designed andclinically applied.

The term “antagonist” refers to any molecule inhibiting the biologicalactivity of the antagonized molecule. Examples of antagonist moleculesinclude, among others, proteins, peptides, natural peptide sequencevariations and small organic molecules (with molecular weight of lessthan 500 Daltons).

The term “normal reference values” used in the present invention refersto the level of certain proteins, mRNA or other metabolites of the bodypresent in a healthy individual.

The term normal tissue used in the present invention refers to anon-cancerous tissue, including commercial cell cultures.

The present invention is based on the discovery that the choline kinasealpha protein expression increases in tumor processes, and especially inlung, breast and colorectal cancers. As well as on the surprisingdiscovery that the overexpression of said protein induces tumors in vivoand therefore that the inhibition of the expression and/or activity ofthis enzyme is an excellent method for the treatment of cancer,especially for lung, breast and colorectal cancer. Choline kinase alphatherefore is a good potential therapeutic target in human tumorigenesis.

In this sense, the present invention provides in the first place an invitro method for detecting the presence of cancer in an individual,preferably lung, breast or colorectal cancer, for determining the stageor severity of said cancer in the individual, or for monitoring theeffect of the therapy administered to an individual having said cancer,comprising:

-   -   a) the detection and/or quantification of the choline kinase        alpha protein, of the mRNA of the choline Kinase alpha gene or        the corresponding cDNA in a sample of said individual, and    -   b) the comparison of the amount of choline kinase alpha protein,        the amount of mRNA of the choline kinase alpha gene or the        amount of the corresponding cDNA detected in a sample of an        individual; with the amount of choline kinase alpha protein,        with the amount of the mRNA of the choline kinase alpha gene or        with the amount of the corresponding cDNA detected in the        samples of control individuals or in earlier samples of the same        individual or with the normal reference values.

The method provided by the present invention has high sensitivity andspecificity, and is based on subjects or individuals diagnosed withcancers, preferably lung, breast and colorectal cancers, having hightranscribed mRNA levels of the choline kinase alpha gene, or highconcentrations of the protein encoded by the choline kinase alpha gene(choline kinase alpha protein), in comparison with the correspondinglevels in samples from subjects with no medical history of thesecarcinomas. However, the expression in humans of the choline kinase betagene is not correlated with any of the previously mentioned types ofcancer.

The present method comprises a step for obtaining the sample from theindividual. Different fluid samples can be worked with, such as forexample; urine, blood, plasma, serum, pleural fluid, ascitic fluid,synovial fluid, bile, gastric juice, cerebrospinal fluid, feces, saliva,bronchoscopy sample fluids, etc. The sample can be obtained by anyconventional method, preferably surgical resection.

The samples can be obtained from previously diagnosed or not diagnosedsubjects, with a certain type of cancer; or also from a subjectundergoing treatment, or who has been previously treated for a cancer,particularly for lung, breast or colorectal cancer.

The present method further comprises a sample extraction step, eitherfor obtaining the protein extract from the sample or for obtaining thetotal RNA extract. One of these two extracts represents the workingmaterial for the next phase. The protocols for extracting the totalprotein or total RNA are well known by the person skilled in the art(Chornczynski P. et al., Anal. Biochem., 1987, 162; 156; ChornczynskiP., Biotechniques, 1993, 15: 532; Molina, M. A., et al., Cancer Res.,1999, 59: 4356-4362).

Any conventional assay can be used in the framework of the invention fordetecting a cancer, provided that it measures in vitro the transcribedmRNA levels of the choline kinase alpha gene or its complementary cDNA,the concentration of the choline kinase alpha protein in samplescollected from the individuals to be analyzed and from controlindividuals.

Therefore, this invention provides a method for detecting the presenceof cancer, especially lung, breast or colorectal cancer, for determiningthe stage or severity of said cancer in the individual, or formonitoring the effect of the therapy administered to an individualhaving said cancers, either based on the measurement of theconcentration of the choline kinase alpha protein, or on the measurementof the choline kinase alpha gene expression level.

In the event that the intention is to detect the choline kinase alphaprotein, the method of the invention comprises a first step for placingthe protein extract from the sample into contact with a composition ofone or more specific antibodies against one or more epitopes of thecholine kinase alpha protein, and a second step for quantifying thecomplexes formed by antibodies and the choline kinase alpha protein.

There is a wide variety of immunological assays available for detectingand quantifying the formation of specific antigen-antibody complexes; anumber of competitive and non-competitive protein binding assays havebeen previously described, and a large number of these assays arecommercially available.

Therefore, the choline kinase alpha protein can be quantified withantibodies such as, for example: monoclonal antibodies, polyclonalantibodies, either intact or fragments thereof, “combi-bodies” and Fabor scFv fragments of antibodies specific against the choline kinasealpha protein; these antibodies being human, humanized or of a non-humanorigin. The antibodies used in these assays can be marked or unmarked;the unmarked antibodies can be used in agglutination assays; the markedantibodies can be used in a wide variety of assays. The markingmolecules that can be used to mark the antibodies includeradionucleotides, enzymes, fluorophores, chemiluminescent reagents,enzymatic substrates or cofactors, enzymatic inhibitors, particles, dyesand derivatives.

There is a wide variety of well known assays which can be used in thepresent invention using non-marked antibodies (primary antibody) andmarked antibodies (secondary antibody); these techniques include Westernblot, ELISA (Enzyme-Linked Immunosorbent assay), RIA (Radioimmunoassay),competitive EIA (Competitive enzyme immunoassay), DAS-ELISA (Doubleantibody sandwich-ELISA), immunocytochemical and immunohistochemicaltechniques, techniques based on the use of protein biochips ormicroarrays including specific antibodies or assays based on colloidalprecipitation in formats such as dipsticks. Other ways of detecting andquantifying the protein EFNB2 or the protein EDNRA include affinitychromatography techniques, ligand binding assays or lectin bindingassays.

The preferred immunoassay in the method of the invention is a doubleantibody sandwich-ELISA (DAS-ELISA) assay. Any antibody or combinationof antibodies, specific against one or more epitopes of the cholinekinase alpha protein can be used in this immunoassay. As an example ofone of the many possible formats of this assay, a monoclonal orpolyclonal antibody, or a fragment of this antibody, or a combination ofantibodies, which coat a solid phase are placed in contact with thesample to be analyzed and are incubated for a suitable time and insuitable conditions for forming the antigen-antibody complexes. After awashing in suitable conditions to eliminate the non-specific complexes,an indicator reagent, comprising a monoclonal or polyclonal antibody ora fragment of this antibody, or a combination of these antibodies,bonded to a signal generating compound is incubated with theantigen-antibody complexes under suitable conditions and for a suitabletime. The presence of the choline kinase alpha protein in the sample tobe analyzed is detected and quantified, should it exist, by measuringthe generated signal. The amount of choline kinase alpha protein presentin the sample to be analyzed is proportional to that signal.

In the event that the intention is to detect the mRNA or cDNAcorresponding to the choline kinase alpha gene, and not the proteinsthey encode, the method of the invention for detecting in vitrocarcinoma has various steps. Therefore, once the sample is obtained andthe total RNA is extracted, the method of the invention, the detectionof mRNA or of the corresponding cDNA of the choline kinase alpha gene,comprises a first step of amplifying the mRNA present in the total RNAextract, or the corresponding cDNA synthesized by reverse transcriptionof the mRNA, and a second step of quantifying the amplification productof the mRNA or cDNA, of the choline kinase alpha gene.

An example of amplifying themRNA consists of retrotranscribing the mRNAinto cDNA (RT), followed by polymerase chain reaction (PCR); PCR is atechnique for amplifying a certain nucleotide sequence (target)contained in a mixture of nucleotide sequences. An excess pair ofoligonucleotide primers which hybridize with the complementary strandsof the target nucleotide sequence is used in the PCR. Then an enzymewith polymerase activity (DNA Taq Polymerase) extends each primer usingas a mold the target nucleotide sequence. The extension products arethen converted into target sequences after disassociation of theoriginal target strand. New primer molecules hybridize and thepolymerase extends them; the cycle is repeated to exponentially increasethe number of target sequences. This technique is described in U.S. Pat.No. 4,683,195 and U.S. Pat. No. 4,683,202. Many methods for detectingand quantifying PCR amplification products have been previouslydescribed and any of them can be used in this invention. In a preferredmethod of the invention, the amplified product is detected by agarosegel electrophoresis.

In another example, the detection of the mRNA is carried out bytransferring the mRNA to a nylon membrane by means of transfertechniques such as for example Northern blot, and detecting it withspecific probes of the mRNA or the corresponding cDNA of the cholinekinase alpha gene.

In a particular embodiment, the amplification and quantification of themRNA corresponding to the choline kinase alpha gene is carried out atthe same time by means of real-time quantitative RT-PCR (Q-PCR).

The last step of the method of the invention for detecting in vitro thecarcinomas in question in a sample from an individual comprisescomparing the amount of choline kinase alpha protein, the amount of mRNAof the choline kinase alpha gene or the amount of the corresponding cDNAof the sample from an individual, with the amount of choline kinasealpha protein, the amount of mRNA of the choline kinase alpha gene orthe amount of the corresponding cDNA detected in the samples of controlsubjects or in earlier samples of the same individual, or with thenormal reference values.

In a second object, the invention also provides an in vitro method foridentifying and evaluating the effectiveness of compounds for cancertherapy; preferably for lung, breast or colorectal cancer, comprising:

-   -   a) placing a culture of tumor cells, preferably lung, breast,        colon or rectal tumor cells, in contact with the candidate        compound, under the suitable conditions and for the suitable        time to allow them to interact,    -   b) detecting and quantifying the expression levels of the        choline kinase alpha gene or the choline kinase alpha protein,        and    -   c) comparing said expression levels with those of the control        cultures of tumor cells not treated with the candidate compound.

The quantification of the expression levels of the choline kinase alphagene or the choline kinase alpha protein is carried out similarly tothat indicated in the method of the invention for detecting in vitro thepresence of lung, breast or colorectal cancer in an individual.

When an agent reduces the choline kinase alpha gene expression levels orreverses the effects of the high expression of said gene, preferablyreducing the cell proliferation levels, this agent becomes a candidatefor cancer therapy.

Therefore, another object of the invention refers to the use ofnucleotide or peptide sequences derived from the choline kinase alphagene in methods of finding, identifying, developing and evaluating theeffectiveness of compounds for cancer therapy, especially for lung,breast or colorectal cancer. It is essential to point out the importancethat has recently been acquired by drug screening methods based on thecompetitive or non-competitive binding of the potential drug molecule tothe therapeutic target.

Another additional object of the invention refers to the use ofnucleotide or peptide sequences derived from the choline kinase alphagene for detecting the presence of cancer, especially lung, breast orcolorectal cancer, for determining the stage or severity of said cancersin the individual, or for monitoring the effect of the therapyadministered to an individual having any of these cancers.

Another object of the invention consists of providing agentscharacterized in that they inhibit the expression and/or activity of thecholine kinase alpha protein. These agents, which can be identified andevaluated according to the present invention, can be selected from thegroup formed by:

a) an antibody, or combination of antibodies, specific against one ormore epitopes present in the choline kinase alpha protein, preferably ahuman or humanized monoclonal antibody; also being able to be a fragmentof the antibody, a single-chain antibody or an anti-idiotype antibody,

b) cytotoxic agents, such as toxins, molecules with radioactive atoms,or chemotherapeutic agents, including but not limited to small organicand inorganic molecules, peptides, phosphopeptides, anti-sensemolecules, ribozymes, siRNAs, triple helix molecules, etc., inhibitingthe expression and/or activity of the choline kinase alpha protein, and

c) antagonist compounds of the choline kinase alpha protein, inhibitingone or more of the functions of the choline kinase alpha protein.

A pharmaceutical composition comprising a therapeutically effectiveamount of one or several of the previously mentioned agents togetherwith one or more excipients and/or carrier substances also constitutesan object of the present invention. Furthermore, said composition maycontain any other active ingredient that does not inhibit the functionof the choline kinase alpha protein.

The excipients, carrier substances and auxiliary substances must bepharmaceutically and pharmacologically tolerable, such that they can becombined with other compounds of the formulation or preparation and donot have any adverse effects on the treated organism. The pharmaceuticalcompositions or formulations include those which are suitable for oralor parenteral administration (including subcutaneous, intradermal,intramuscular and intravenous), although the best administration routedepends on the patient's condition. The formulations can be in the formof single doses. The formulations are prepared according to knownmethods in the field of pharmacology. The amounts of active substancesto be administered may vary according to the particularities of thetherapy.

A further aspect of the present application consists of a diagnostic kitfor carrying out the present invention. Therefore, in a particularembodiment, the present invention includes a kit comprising an antibodyespecially recognizing the choline kinase alpha protein and a carrier ina suitable container. In another particular embodiment, this kit is usedfor detecting the presence of cancer in an individual, preferably lung,breast or colorectal cancer, for determining the stage or severity ofsaid cancer in the individual, or for monitoring the effect of thetherapy administered to an individual having said cancer.

A final aspect of the present invention consists of an in vitro methodfor diagnosing the survival time of a patient with breast, lung orbladder cancer comprising the evaluation of the choline kinase alphaprotein expression level in a sample of the cancerous tissue extractedfrom the patient by means of determining in said sample at least oneparameter related to the choline kinase alpha protein which is selectedfrom the level of its messenger RNA, the concentration of said proteinor the enzymatic activity of said protein, and the comparison of theobtained value with the value corresponding to one or more normalnon-cancerous tissue samples.

The following examples illustrate the invention.

Example 1 Choline Kinase Activity of the Isoforms

As is shown in FIG. 1, both enzymes CKD2 (52 kDa, 457 amino acids) andCKE1 (45 kDa, 395 amino acids) have potent choline kinase activity,determined by their ability to produce phosphorylcholine from choline inthe presence of ATP and magnesium (FIG. 1A). This activity is shown inboth its recombinant form, expressed in E. Coli, and after thetransfection in human HEK293 cells. However, and despite the fact thatboth enzymes have choline kinase activity, the intracellular levels ofphosphorylcholine in live cells are not equally altered, being virtuallyundetectable in the cells which overexpress choline kinase beta (FIG.1B). These results suggest that both physiological regulation andbiological function of these two proteins, and therefore, their behaviorin tumorigenesis, may be differential.

Example 2 Specificity of the Antibody

Polyclonal and monoclonal antibodies recognizing the choline kinasealpha enzyme, a protein which has been semi-purified and expressed as anantigen in generation phase and as production control in the remainphases of the process, have been developed. Despite having beendeveloped against choline kinase alpha, due to the fact that bothenzymes (CKα and CKβ) have 65% overall homology throughout theirsequence, and in some conserved regions such as the choline binding andcatalytic activity domains homology reaches 75%, it is necessary tocheck which isoenzymes are able to recognize the generated polyclonaland monoclonal antibodies. we have verified that both the polyclonal andmonoclonal antibodies used are specific for choline kinase alpha andthat they do not recognize choline kinase beta. To that end both cholinekinase alpha and beta proteins were overexpressed in human HEK293Tcells, and after checking that the two proteins are present and active(FIG. 2A), their analysis was carried out by immunodetection techniques(Western blot) with both the polyclonal antibody with which priorstudies were carried out (Ramirez de Molina, A., Gutiérrez, R., Ramos,M. A., Silva, J. M., Silva, J., Sánchez, J. J., Bonilla, F., Lacal, J.C. Oncogene 21, 4317-4322 (2002); Ramirez de Molina, A.,Rodriguez-González, A., Gutiérrez, R., Martinez-Piñero, L., Sanchez, J.J., Bonilla, F., Rosell, R., Lacal, J. C. Biochem. Biophys. Res. Commun.296, 580-583 (2002)], and with the new monoclonal antibodies generatedagainst choline kinase alpha. As is shown in FIG. 2B, which shows anexample with two of these antibodies, even by overexpressing cholinekinase beta in conditions in which the activity is increased 80 times,none of the antibodies recognizes this isoform, choline kinase alphabeing highly recognized in both the same conditions and in theendogenous control levels in all cases. These results indicate that theprior studies of the group in which the polyclonal antibody was useddefine choline kinase alpha as the isoenzyme overexpressed in cell linesderived from human tumors and in the analyzed tumors themselves.

These results were not expected given that by definition, polyclonalantibodies recognize different epitopes in the molecule and the cholinekinases alpha and beta sequences are 65% homologous, in some regionsreaching up to 75%, especially in the consensus domain regions where thecatalytic region and the substrate and ATP binding region are located.

Example 3 Specificity for Tumors: Alteration of Choline Kinase Alpha inDifferent Human Tumors

The availability of antibodies with proven specificity against cholinekinase alpha has allowed studying the possible alteration in cholinekinase alpha expression in some of the most important tumors today indeveloped countries, such as breast, colon, and lung cancer. To carryout this study, paraffin sections of samples from between 38 and 50different patients, each of whom had one of these types of cancer, werecarried out and choline kinase alpha expression has been analyzed bymeans of immunohistochemistry (IHQ), a technique which allows detectingand identifying “in situ” biomolecular components which are an integralpart of cells and tissues and which can be carried out in an automatedmanner in the Pathological Anatomy Department of any hospital. In thebreast, colon or lung samples of these patients, it was found that:

-   -   In all cases, staining of the tumor with the antibody        recognizing choline kinase alpha is highly specific, allowing        the clear distinction between the tumor tissue and the normal        adjacent tissue.    -   There is no case in which the normal tissue stains.    -   The choline kinase alpha enzyme is overexpressed with an        incidence ranging between 62% and 100% in this type of tumor,        demonstrating the high involvement of this isoform, choline        kinase alpha, in human tumorigenesis.

In FIG. 3 an example of the results obtained for large cell lung cancer(NSCLC), which today involves 80% of the cases of lung cancer, can beobserved. As can be observed, cytoplasmic staining of choline kinasealpha, specific for the tumor nodes and which as previously indicatedspecifically stains 62% of the samples, occurs.

Following this concept, a similar study has been carried out in 38patients with breast cancer, the overexpression of choline kinase alphaspecifically in tumor tissue in 97% of the cases again being observed(FIG. 4).

Finally, the study of choline kinase alpha expression in colon cancerhas also been carried out, for which purpose paraffin sections of 40samples from different patients with colon cancer with over 4 years offollow-up have been carried out. The analysis began with carcinomas insitu in stages I, II, III and IV. Similar to the previous case, thenormal tissue of each preparation adjacent to the tumor tissue has beenused as normal tissue. Positive staining in the normal tissues was notobtained in any case in any of the 40 samples, confirming the highspecificity of choline kinase alpha staining in the tumor tissue, inwhich overexpression of the enzyme was again observed in all cases (FIG.5A). These results support the high involvement of this isoform of thisenzyme in colon cancer. Furthermore, this result led to the analysis ofpre-neoplastic lesions, ACFs and polyps with different degrees ofdysplasia, in which the results clearly show that choline kinase alphaoverexpression is an early event in the colon tissue tumor process whichoccurs as of the time of dysplasia, suggesting its potential behavior asa “gate-keeper” gene in these tumors and therefore its relevance as apotential new therapeutic target. FIG. 5B shows a polyp in which it canbe seen how the staining in the normal tissue is virtually undetectable,and as the dysplasia begins to occur (binuclear cells) the stainingincreases, becoming more intense in the mass of the tumor.

Example 4 Specificity for Tumors: Oncogenic Behavior of the CholineKinase Alpha Enzyme

Given the very high incidence of dysregulation of choline kinase alphain some of the most important human tumors today, a study was carriedout to determine if this protein alone has oncogenic ability, i.e. ifcholine kinase alpha has oncogenic activity. To carry out this study, itwas first studied if this gene confers growth capacity in anattachment-independent medium, which involves measuring its transformingcapacity. Human HEK293T cells were transfected with an empty vector ascontrol and with a choline kinase alpha expression vector, and wereseeded in soft agar. As can be seen in FIG. 6, the overexpression ofthis protein is enough to induce oncogenic transformation of both humanHEK293T cells and of epithelial dog MDCK cells.

Given that choline kinase alpha has transforming activity in human.HEK293T cells, their oncogenic potential was analyzed in vivo. To thatend, immunodepressed mice (Nu/Nu) were injected with a million humanHEK293T cells which overexpressed either the empty vector as a control,or the choline kinase alpha expression vector. Tumor growth wasmonitored at least twice a week for 50 days after the injection. Whilethe control cells did not induce any tumor in any of the injected mice,the cells which overexpressed choline kinase alpha induced tumors in 8of the 30 injected mice (26%), which reached a mean of 0.6 cm³ after 45days (FIG. 7). These results show that choline kinase alphaoverexpression is enough to induce tumors in vivo, and therefore is agood potential therapeutic target in human tumorigenesis. To verify ifthe tumors generated by choline kinase alpha maintained their increasedexpression and activity, the tumors were surgically extracted, lysatedand the activity and expression levels of this enzyme were determinedwith respect to those levels of its parent HEK293T cells as control. Ascan be seen in FIG. 8, all the analyzed tumors maintain high expressionand enzymatic activity levels in a manner similar to that which wasobtained before inoculation, showing that choline kinase alphaoverexpression induces tumorigenesis in vivo.

Example 5 Pharmacological Specificity

Once the oncogenic activity of the choline kinase alpha isoform, as wellas its high incidence of overexpression in human tumors was verified, itwas then studied if the anti-tumor effect of the inhibitor MN58b[Hernández-Alcoceba, R., Saniger, L., Campos, J., Núñdez, M. C.,Khaless, F., Gallo, M. Á., Espinosa, A., Lacal, J. C. Oncogene, 15,2289-2301 (1997); Hernández-Alcoceba, R., Fernández, F., Lacal J. C.Cancer Res. 55, 3112-3118 (1999); Ramirez de Molina A., Bañez-CoronelM., Gutiérrez R., Rodriguez González A., Olmeda D., Megias D., Lacal J.C. Cancer Res. 64:6732-6739 (2004)] is specific for this choline kinasealpha isoform or if, in contrast, it could also be attributed to itspossible interaction with the choline kinase beta isoform. Thisverification is necessary because the two choline kinase alpha andcholine kinase beta isoforms share up to 75% homology in the substratebinding domains and in the catalytic region. To that end, the twocholine kinase isoforms (CKα and CKβ) were expressed in the strain of E.Coli bacteria, which lack choline kinase activity, and therefore anyenzymatic activity observed is exclusively due to the recombinantlyexpressed choline kinase isoform. As can be seen in FIG. 9, theenzymatic activity of choline kinase alpha is affected by treatment withMN58b, with a more pronounced effect than the effect exerted by the sameinhibitor on the p isoform. In fact, MN58b is 20 times more activeagainst choline kinase alpha that it is against choline kinase beta.

Given that tumors have been generated in vivo by overexpressing cholinekinase alpha and that MN58b is specific for this isoform, it has beenverified if the growth of the tumors induced by ChoKα is susceptible toinhibition by MN58b. To that end, a million human HEK293T cellstransfected with the cka gene which showed a high overexpression of thecholine kinase alpha enzyme were subcutaneously injected inimmunodepressed Nu/Nu mice. When the tumors reached a tumor volume of0.1 cm³, treatment with the specific choline kinase alpha inhibitor,MN58b, began, which was administered intraperitoneally in sterilephysiological serum for 5 consecutive days with 9 days of rest at a doseof 5 mg/Kg. The control mice received equivalent carrier doses,following the same calendar and the tumors were monitored at least twicea week. As shown in FIG. 10, choline kinase alpha inhibition results ina strong inhibition of tumor growth, reaching 80% tumor growthreduction. These results show that not only is choline kinase alphaoverexpression enough to induce tumors in vivo, but the proliferation oftumor cells depends on choline kinase alpha activity.

Example 6 Genetic Specificity

All these results support the potential of choline kinase alpha as a newtherapeutic target for the design of a new anti-tumor strategy. However,chemical inhibitors can carry out their antiproliferative action bymeans of effects that are concealed from the investigator, even thoughthey are designed specifically against a certain enzyme, as is the caseof the inhibitor MN58b. There are a number of cases in the literature inwhich it is shown that inhibitors designed specifically against a kinasealso affect other kinases which are not even closely related to oneanother. There is an approach recently developed in the past few yearsthat allows more precisely establishing the effects of interference witha particular enzyme by means of the use of siRNA (small interferenceRNA) which are capable of precisely and selectively eliminating mRNA fora certain protein without affecting the remaining cell proteins. In thiscase it was verified that pharmacological interference by means of theuse of the inhibitor MN58b, specific against choline kinase alpha, hasconfirmation at the genetic level by means of the specific inhibition ofcholine kinase alpha by the siRNA technique. This technique would allowdefinitively validating ChoKα as a new therapeutic target in cancer. Forthis purpose, an oligonucleotide capable of hybridizing with the cholinekinase alpha messenger RNA (which has been called siCHKA), and thereforecapable of specifically blocking expression of this protein, wasgenerated. It was first verified that this siRNA efficiently blockscholine kinase alpha expression in human HEK293T cells, both theendogenous protein and a ChoKα fused to GST and transfected in the samecells (FIG. 11).

Once it was verified that this interference RNA specific to cholinekinase alpha is truly capable of efficiently blocking the expression ofthis protein, its effect in the tumor cells derived from a human breastcarcinoma, MIDA-MI3-231, in which it was previously described that thepharmacological inhibition of choline kinase with MN58b induced a stronganti-tumor effect due to apoptosis induction, was then verified. As canbe seen in FIG. 12, despite the lower transfection efficiency obtainedin these cells, it was observed that the transfection of siCHKA inMDA-MB-231 implies inhibition of both choline kinase alpha expressionand of its enzymatic activity. To verify that the effect of geneticinhibition of choline kinase alpha by means of siRNA is similar to thatobtained by means of pharmacological inhibition with MN58b, thusunequivocally demonstrating the specificity of the effect on cholinekinase alpha, cell viability after transfection with interference siCHKAwas determined. As occurs after treatment of the tumor cells with MN58b,a reduction in cell viability is observed associated to death due toapoptosis which is specific for the cells transfected with the cholinekinase alpha interference agent (FIG. 13).

Finally, as occurs with RMN58b, it was verified that the expression ofinterference siCHKA, specific for choline kinase alpha, has no effect onthe viability of normal primary human mammary cells HMEC (human mammaryepithelial cells). In these cells, baseline expression of this proteinis very low given that, as previously described, the tumor cellsconstitutively overexpress choline kinase alpha. However, despite thislow baseline expression of choline kinase alpha in the primary cellsHMEC, clear interference of the expression of the choline kinase alphaenzyme is obtained, and it can be observed how these cells, unlike whatoccurs in the tumor cells, do not die due to apoptosis, but they arecycle-arrested (FIG. 14), a result which is identical to that observedin the same cells treated with the inhibitor PAN58b [Rodriguez-GonzálezA., Ramirez de Molina A, Fernández F., Ramos M. A., Nuñez, M. del C.,Campos, J. M, Laca. J. C. Oncogene 22:8803-8812 (2003);Rodriguez-González A, Ramirez de Molina A, Fernández F., Lacal J C.Oncogene 23:8247-8259 (2004); Rodriguez-González A., Ramirez de MolinaA., Bañez-Coronel M., Megias D., Núñez M. C and Lacal J. C Int. J. Oncol26:999-1008 (2005)].

Example 7 Effect of Choline Kinase a on Breast Cancer Incidence inSurvival

In order to have quantitative data confirming the involvement of cholinekinase a in the generation and evolution of tumors, additional assaysquantifying their expression in patients with the types of cancer withwhich choline kinase a seems to be specifically related (breast, lungand bladder cancer) and their possible relationship with the prognosisof the evolution of said patient were carried out.

On one hand quantitative analysis of choline kinase a expression wascarried out by isolating messenger RNA from patient samples. To thatend, automated real-time quantitative PCR reactions were carried outwith specific Taqman probes which only recognize the messenger RNAobject of study, the messenger RNA corresponding to ChoKα. The obtaineddata is represented in base 10 logarithmic scale with respect to acontrol sample of normal tissue.

In the case of data obtained in relation to breast cancer, the obtainedresults are shown in FIG. 15 a. It can be observed that the samples withlevels above the median ChoKα activation correspond to those patientswith a worse prognosis (presence of lymphatic nodes, development ofmetastasis, lower survival). This data is confirmed with the data inFIGS. 15 b and 15 c. In FIG. 15 b, prepared with the data obtained in 63patients with breast cancer, it can be observed how the mean value ofChoKα expression (calculated as relative expression units of the gene,calculated from the mRNA level with the 2^(−ΔΔct) method (Livak, K. J.and Schmitttgen, T. D. (2001) Analysis of relative gene expression datausing real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.Methods 25, 402-408)) is much higher in patients presenting metastasisin comparison with those patients who do not. If the probability ofsurvival of these patients is represented according to the presence oflymphatic nodes, which is significantly associated to an increase inChoKα expression with respect to the controls (p<0.001), it can beobserved in a classic Kaplan Meier curve (Kaplan E L, Meier 2,Nonparametric estimation from incomplete observations. J. Am. Stat.Assoc., 53:457-481 (1958)) how the probability of survival significantlydecreases as the presence of positive lymphatic nodes increases(p=0.046) (FIG. 15 c), the same trend being observed when patientsurvival is represented according to ChoKα expression (p=0.059).

Example 8 Effect of Choline Kinase α in Lung Cancer: OverexpressionLevel and Incidence in Survival

Several tests were carried out to complement the study on the importanceof choline kinase a overexpression in lung cancer.

First, the mRNA levels corresponding to said enzyme in cell linesderived from patients with lung cancer were detected again by means ofautomated real-time quantitative PCR reactions with specific Taqmanprobes. They were carried out both on cell lines corresponding to themost common type of lung cancer (75-85%), non-microcytic or NSCLC (nonsmall cell lung cancer), represented by lines H460 and H1299, and onlines corresponding to the other type of cancer, microcytic or SCLC(small cell lung cancer), represented by lines H510 and H82, the databeing represented in logarithmic scale relating to normal primary humanbronchial epithelial cells, BEC. The results are shown in FIG. 16 a.This data was complemented with the data on the detection of proteinlevels in each of these cell lines by means of immunoassay with amonoclonal antibody (FIG. 16 b) and the data on the detectable enzymaticactivity in the same lines by measuring the radioactively marked product(PCho) generated after 30 minutes from the marked substrate (Cho) (FIG.16 c). An increase with respect to the controls, which is particularlyconsiderable in the case of the SCLC lines, especially H510, is observedin all cases.

The antiproliferative effect of ChoK inhibition in said cell linescaused by the addition of MN58b was also checked, obtaining the resultsshown in the following Table, in which the numbers between parenthesesindicate the sensitivity of each cell compared with the primary cells.The differences between the primary cells and the four cell linesderived from tumors were significant (p:<0.001) in all the analyzed timeperiods.

TABLE 1 Antiproliferative effect of ChoK inhibition against cell linesderived from human lung tumors Cell 1 48 h IC50 (μM) 72 h IC50 (μM) 114h IC50 (μM) Primary BEC 40.5 ± 6.2     18.3 ± 4.8    4.2 ± 0.8   Primary HMEC 44.7 ± 4.95    20.9 ± 2.7    3.4 ± 0.13  NSCLC H1299 10.3 ±2.5 (4)  2.7 ± 0.7 (8) 0.9 ± 0.1 (4) NSCLC H460 7.03 ± 2.03 (6)  2.6 ±0.8 (8) 1.1 ± 0.1 (3) SCLC H510 1.1 ± 0.1 (41)  0.4 ± 0.05 (53)  0.1 ±0.03 (27) SCLC H82 1.9 ± 0.2 (24)  0.8 ± 0.04 (27)  0.27 ± 0.01 (12)

These results were complemented with ChoKα overexpression studies inhuman tumor samples from patients with lung cancer, specifically intissue from patients with NSCLC from whom the tumor was extracted in anearly stage. FIG. 17 shows the results obtained in the real-timequantitative PCR analysis of the messenger RNA corresponding to ChoKα insaid patients who were operated on in early stages, results which showthat in such an early stage of the disease, ChoKα is alreadyoverexpressed with respect to normal tissue in 53% of the cases. Again,when the relationship between ChoKα expression and the severity of thecancer (stage and presence or absence of metastasis) is analyzed, it wasobserved that high ChoKα expression is associated to higher tumormalignancy, as shown in Table 2:

TABLE 2 ChoKα overexpression according to the severity of the lungcancer ChoKα No. and % of No. and % of patients with patients withnormal levels overexpression p Stage IA-IIIA^(a) 18 (60%) 12 (40%) 0.019 IIIB-IV^(b) 0 (0%) 6 (100%) Metastasis No  18 (69.2%)  8 (30.8%)0.0015 Yes 0 (0%) 7 (100%) ^(a)Stages in which the tumor is small, thereis little or no involvement of nodes and no presence of metastasis^(b)Stages with larger tumors with involvement of the nodes and presenceof metastasis

As in the case of breast cancer, in initial stages of NSCLC ChoKαoverexpression in lung cancer is associated to a worse prognosis, as canbe observed in the graphs shown in FIG. 18. It can be seen in suchfigures how the probability of survival is maintained at value 1 overtime in those patients in whom direct ChoKα expression is not detected,whereas in those patients in whom ChoKα overexpression is detected, theprobability decreases, showing a median value of 9 months when thedisease-free survival is evaluated, i.e. the time elapsing from when thepatients are operated on until they experience relapse.

Example 9 Effect of Choline Kinase a on Bladder Cancer: OverexpressionLevel and Incidence on Survival

Analogous studies were also carried out in patients with bladder cancer.First, the mRNA levels corresponding to said enzyme in cell linesderived from patients with bladder cancer were detected, again by meansof automated real-time quantitative PCR reactions with specific Taqmanprobes, similar to that described in Example 8 for the case of lungcancer. Lines HT1376, J82, SW780, TCCSup and UMVC3 were used, the databeing represented in logarithmic scale in relation to normalimmortalized bladder cells, UrotSa. The results are shown in FIG. 19 a.The data was complemented with the detection data regarding the proteinlevel in each of these cell lines by means of immunoassay with amonoclonal antibody (FIG. 19 b) and the assessment of the detectableenzymatic activity therein (FIG. 19 c). It can be observed that thedifferent cell lines show increased ChoKα levels with respect to normalimmortalized UrotSa cells, as well as that the increase of theexpression of the protein in the cell lines derived from bladder canceris also accompanied by a similar increase in the activity of the cholinekinase enzyme.

Additionally, the antiproliferative effect of ChoK inhibition in thesecell lines caused by the addition of MN58b was also checked, obtainingthe results shown in the following Table, in which the numbers betweenparentheses indicate the induction factor with respect to the cell linewith lover ChoK levels, TCCSup, as the data obtained for UrotSA were notconsidered to be sufficiently reliable for carrying out the comparisonin relation thereto.

TABLE 3 Antiproliferative effect of ChoK inhibition against cell linesderived from human bladder cancer Cell line TCCSup HT1376 UMUC3 J82SW780 IC50 3.7 (1) 2.49 (1.5) 1.98 (1.8

1.08 (3.4

0.91 (4.1

(□M) (96 h) ChoK 2.5 (1)  5 (2) 5 (2)  12.6 (5) 12.6 (5) Expres- sionChoK 3.6 81)   7 (1.9) 9 (2.5) 14.5 (4)   15 (4.2) Activity

indicates data missing or illegible when filed

Furthermore, in order to establish parallelisms with the effectsobserved in vivo, ChoKα expression in tumor tissue in 90 patients withbladder cancer was analyzed using microarray technology, specificallythe U133 Plus 2.0 chip of Affymetrix. The obtained results are shown inFIG. 20 a. In said table it can be observed how a little over half, 49patients, showed an expression induction factor of between 1 and 3times; 25 patients showed an expression induction factor of between 3and 8, whereas in 12 of them the expression induction factor was from 8to 24 times.

The data obtained with the microarray were validated by means of areal-time quantitative PCR assay (assay with Taqman probes), the resultsof which are shown in FIG. 20 b. In said assay, commercial RNA fromnormal human bladder tissue was used as a reference, using GAPDH asendogenous control. In 18 of the samples analyzed (10 of whichcorresponded to the 10 patients with lower ChoKα expression and theother 10 corresponded to the patients with the highest expression), theChoK expression results coincided with respect to the Affymetrixmicroarray and the analysis with Tagman probes. The incidence of ChoKαoverexpression in tumors was 55%. The patients with overexpression werethe most metastatic.

The relationship between ChoKα overexpression and the progression ofmetastases was confirmed with the ChoKα expression data from all thepatients obtained from the arrays, the results of which are shown inFIGS. 21 a and 21 b. FIG. 21 a shows the variation in the mean ChoKαexpression levels between the negative and positive patients withrespect to the presence of lymph nodes (values joined by the line withblank squares at the ends) or the development of metastases (valuesjoined by the line with solid circles at the ends), FIG. 21 b, however,shows a graph representing the variation in the proportion of patientswith metastases (bars with continuous dark color,

) and without metastases (bars with slash marks, //) in the groups ofpatients with low ChoKα expression (low (pair of bars on the left),intermediate ChoKα expression (pair of bars located in the middle of thegraph) or high ChoKα expression (pair of bars located on the right sideof the graph), in which it can be seen how the percentage of patientswith metastases (53%) in the low expression group is not much higherthan that of patients without metastases (47%), whereas in the highChoKα expression group, most of them, 72%, have metastasis and theremaining 28% do not. A relationship is observed between ChoKαexpression and the development of metastases which does not reach thelevel of statistical significance.

To demonstrate the relevance of ChoKα overexpression in bladder cancerin vivo, an orthotopic bladder cancer model was also used which isphysiologically very similar to what occurs when a tumor is generated inthe bladder, using MET-2 (mouse bladder tumor) cells. In these cells,which already have overexpressed ChoKα with respect to normal mousecells, this protein is even more overexpressed for the purpose ofevaluating if a greater ChoKα expression enhances the aggressiveness orinvasiveness of these tumors. To that end, MET-2 cells containing anempty vector, lacking sequences which allowed expressing the ChoKα gene(control group of mice, consisting of three mice), or MBT-2 cellsoverexpressing ChoKα by having been transfected with a vector with thesequence encoding for said enzyme (ChoKα group of mice, consisting ofthree mice), were directly inoculated in the bladder of the mice bymeans of a catheter. The generation of tumors was monitored in bothgroups by means of nuclear magnetic resonance with gadolinium contrast,as well as the evolution of the disease in the mice (physical condition,survival, histological study of the tumors, analysis of the possibleinvasion of the kidney and other organs . . . ). 19 days afterinoculating the cells, the ChoKα mice were in a poor condition, 2 ofthem with a very large tumor, whereas the mice that received the emptyvector (control group) began to have a poor condition 50 days afterinoculating the cells.

The results of Examples 7, 8 and 9 confirm that ChoKα is overexpressedwith a high incidence in human breast, lung and bladder tumors. Itsoverexpression is associated with clinical parameters indicating greatermalignancy: presence of lymphatic nodes, metastasis and low patientsurvival.

Example 10 Genetic Specificity: Inducible Interference Model

Given that the interference of ChoKα in tumor cells is lethal inducingcell death by apoptosis, as demonstrated in the assays described inExample 6, carried out in a transient assay, it is not possible to havea stable cell population expressing the interference construction inthis type of study. A percentage of the variable cell population isaffected in transient assays, the total population never being affected,which masks the results. It would be better to study the effect of theconstruction on a population that expressed it homogenously, so it wouldnot be necessary to have a stable constitutional model. This makes itnecessary to have an inducible interference model which allows obtaininga homogenously interfered population in ChoKα expression.

To obtain this, the interference sequence is expressed in a constructionin which it is under a repressor which prevents its expression. Theco-transfection of the inducible construction of interest together witha repressor which prevents its expression is carried out, and once ahomogenous population is selected with this construction, the cells aretreated with an inducer, which allows the expression of the interferenceof the construction and therefore the interference of the expression ofthe protein.

In the inducible model designed for this assay, the interferenceconstruction for ChoKα is expressed in the vector pSUPERIOR-pure(Oligoengine) and the repressor in the vector pcDNA6/TR (Invitrogen).The inducer used is doxocycline which, when binding to the repressor,prevents it from binding to the corresponding sequence, therefore theexpression of the interference sequence is no longer prevented. A schemeof this system can be observed in FIG. 22.

FIGS. 23 and 24 show the results obtained in Ch-ind-1 cells, a cell linederived from MDA-MB-231, capable of expressing the interferenceconstruction after treatment with the inducing agent doxocycline. FIG.23 shows that this inducible line is still sensitive to the chemicalinhibition of ChoKα in a manner similar to what occurs in MDA-MB-231(the parent control line derived from breast adenocarcinoma from whichCh-ind-1 is generated), as the results obtained after treatment with thecholine kinase inhibitors MN58b or RSM936 are analogous in both lines.FIG. 24, however, shows how the genetic inhibition of ChoKα occurs onlyin Ch-ind-1 when treating both cell lines with 10 μg/ml of doxocycline,as the induction of the interference model with doxocycline can onlyoccur in line Ch-ind-1, because it is the one having a construction fromwhich the synthesis of interference RNA can occur when the binding ofthe repressor is prevented. The genetic inhibition of ChoKα iscorrelated with a reduction of cell proliferation (determined by pCNA)and an increase of cell death due to apoptosis (determined by PARPdig,degraded PARP protein, which is an indicator of apoptosis). The effectbegins to be seen after 10 days, although it is still very initial, andis much more pronounced 20 days after the beginning of the experiment(in which the population has very little ChoKα expression).

The results obtained with the inducible model corroborate the datapreviously obtained in transient, showing that the observed effects aredue to the specific inhibition on ChoKα.

Example 12 Evaluation of the Possible Effect of Chokβ Overexpression inCarcinogenesis

Several assays were carried out to evaluate the possible effect thatcholine kinase beta (ChoKβ) overexpression may have in carcinogenesisand to confirm if the increase of choline kinase activity observed indifferent cancerous tissues and cell lines derived from canceroustissues could be attributed exclusively to choline kinase alpha or ifcholine kinase beta also participated.

First a polyclonal anti-ChoKβ1 antibody was generated. The specificitythereof was checked in three groups of transfected Hek293T cells, one ofwhich was transfected with a construction from which ChoKα expressionwas produced, a second one transfected with a construction that allowedthe expression therein of ChoKβ, and the third one with a constructionin which a chimeric protein ChoKa-GFP was expressed, as well as in agroup of control cells transfected with an empty vector. As can be seenin part A of FIG. 25, the immunodetection assays showed the specificityof said antibody, which gave way to a signal both in the cells thatexpressed ChoKβ and in the cells that expressed the chimeric proteinChoKβ-GFP, without a signal occurring in the lane corresponding to thecells transfected with the construction for ChoKα expression; in theselatter cells, however, a monoclonal antibody directed against ChoKα giverise to a signal in a band which occurred at the height corresponding toChoKα.

In order to check the possible effect of ChoKβ on carcinogenesis, itpossible transforming activity was assayed in vivo. To that end, athymicmice (Nu/Nu) were used again that were injected with a milliontransfected human HEK293T cells, either with an empty vector as acontrol, with a choline kinase alpha expression vector, or with acholine kinase beta expression vector and, in a last group, theco-transfection of the vectors which expressed each of the cholinekinase alpha and beta isoenzymes was produced. The tumor growth wasmonitored at least twice a week for 13 weeks after the injection. As canbe observed in FIG. 26, a clear induction of tumors was observed in theanimals that had received the cells transfected with the ChoKαexpression vector, no induction of tumors being observed in the micethat received the cells transfected with the ChoKβ expression vector. Itis striking to observe that in the mice that received cells transfectedwith both vectors, the ChoKα and ChoKβ expression vectors, a slightinduction of tumors was observed with a magnitude that was much lessthan that observed with ChoKα expression alone and observed more than 11weeks after the injection of the transfected cells, which may indicatedthat ChoKβ may be directly or indirectly regulating ChoKα such that itinhibits its oncogenic activity.

This data was complemented by seeing if there was overexpression of thecholine kinase beta enzyme in tissues extracted from patients withcancer. FIG. 27 shows the data obtained in lung samples from patientsoperated on after isolating messenger RNA therefrom and carrying outautomated real-time quantitative PCR reactions with specific Taqmanprobes, representing the obtained data in a base 10 logarithmic scalewith respect to a normal tissue control sample. In said figure it can beobserved how ChoKβ expression decreases with respect to that obtained innormal tissue in most of the analyzed samples, unlike what occurs withChoKα.

This data does not suggest that there was a correlation between cholinekinase beta overexpression and the generation and development of tumors.

All the results indicated in the examples specifically support cholinekinase alpha as a new therapeutic target in the treatment of neoplasticdiseases.

1. An in vitro method for identifying and evaluating the effectivenessof compounds for cancer therapy comprising: a) placing a culture oftumor cells in contact with the candidate compound, under the suitableconditions and for the suitable time to allow them to interact, b)detecting and quantifying the expression levels of the choline kinasealpha gene or the choline kinase alpha protein, and c) comparing saidexpression levels with those of the control cultures of tumor cells nottreated with the candidate compound.
 2. The in vitro method according toclaim 1 wherein the cancer is selected from the group consisting of lungcancer, breast cancer, colorectal cancer or bladder cancer.
 3. An agentthat inhibits the expression and/or activity of the choline kinase alphaprotein, or ill that they inhibit the carcinogenic effects of cholinekinase alpha protein overexpression.
 4. The agent according to claim 3,selected from the group formed by: a) an antibody, or combination ofantibodies, specific against one or more epitopes present in the cholinekinase alpha protein; a fragment of an antibody or an antibody chain, b)cytotoxic agents inhibiting the carcinogenic effects of theoverexpression and/or activity of the choline kinase alpha protein, andc) antagonist compounds of the choline kinase alpha protein, inhibitingthe carcinogenic effects of the expression and/or activity of thecholine kinase alpha protein.
 5. A method for the treatment of cancer,comprising administering to a patient in need of such treatment atherapeutically effective amount of the agents according to claim
 3. 6.The method according to claim 5 wherein the cancer is selected from thegroup consisting of lung cancer, breast cancer, colorectal cancer orbladder cancer.
 7. A pharmaceutical composition comprising atherapeutically effective amount of one or several agents according toclaim 3 together with at least one pharmaceutically acceptableexcipient.
 8. The pharmaceutical composition according to claim 7,wherein it contains another active ingredient.
 9. The pharmaceuticalcomposition according to claim 8 wherein said another active ingredientis an agent which does not inhibit the function of the choline kinasealpha protein.
 10. (canceled)
 11. (canceled)
 12. (canceled)
 13. An invitro method of monitoring the effect of a therapy administered to acancer patient, the method comprising a) evaluating the choline kinasealpha protein expression level in a tissue sample extracted from thepatient who is being administered an anti-tumor agent, preferably anagent, by means of the determination in said sample of at least oneparameter related to the choline kinase alpha protein which is selectedfrom the level of its messenger RNA, the concentration of said proteinor its enzymatic activity, and b) the comparison of the obtained valuewith the value corresponding to one or more normal non-cancerous tissuesamples. 14.-16. (canceled)
 17. The method according to claim 13 whereinthe anti-tumor agent is an agent that inhibits the expression and/oractivity of the choline kinase alpha protein, or that inhibit thecarcinogenic effects of choline kinase alpha protein overexpression. 18.The method according to claim 13 wherein the anti-tumor agent ispharmaceutical composition comprising a therapeutically effective amountof one or several agents that inhibit the expression and/or activity ofthe choline kinase alpha protein, or that inhibit the carcinogeniceffects of choline kinase alpha protein overexpression, together with atleast one pharmaceutically acceptable excipient.
 19. The agent accordingto claim 4 wherein the antibody or combination of antibodies, specificagainst one or more epitopes present in the choline kinase alpha proteinis a human or a humanized monoclonal antibody.
 20. The agent accordingto claim 4 wherein the cytotoxic agents is selected from the groupconsisting of toxins, molecules with radioactive atoms, chemotherapeuticagents, peptides, phosphopeptides, anti-sense molecules, ribozymes,triple helix molecules, double strand RNA, and siRNA.